Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.9.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21043	0.315
27DAP/17DAP	0.97517	0.853
39DAP/27DAP	1.10491	1
41DAP/39DAP	0.99216	0.866
42DAP/41DAP	0.92235	1
43DAP/42DAP	1.26611	0.768
47DAP/43DAP	1.09804	0.92
52DAP/47DAP	1.54287	0.584
57DAP/52DAP	1.20401	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13144	0.662
17DAP/reference	1.1248	0.028
27DAP/reference	1.00401	0.904
39DAP/reference	1.10471	0.262
41DAP/reference	1.10322	0.221
42DAP/reference	0.85119	0.023
43DAP/reference	0.99519	0.861
47DAP/reference	0.86198	0.023
52DAP/reference	0.76105	0.065
57DAP/reference	0.71376	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11964	0.91
27DAP/17DAP	1.10729	0.761
39DAP/27DAP	1.07306	0.646
41DAP/39DAP	0.95903	0.923
42DAP/41DAP	0.92871	0.538
43DAP/42DAP	1.01546	1
47DAP/43DAP	0.97049	0.877
52DAP/47DAP	0.97491	0.913
57DAP/52DAP	1.19332	0.378
57DAP/7DAP	0.94366	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.60925	0.032
17DAP/reference	1.46324	0.006
27DAP/reference	1.45288	0.026
39DAP/reference	2.05358	0.005
41DAP/reference	1.33612	0.05
42DAP/reference	1.40556	0.014
43DAP/reference	1.3601	0.017
47DAP/reference	0.95416	0.504
52DAP/reference	1.32186	0.062
57DAP/reference	1.54448	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18286	0.102
17DAP/reference	1.10314	0.338
27DAP/reference	1.04189	0.974
39DAP/reference	0.93888	0.348
41DAP/reference	0.82087	0.112
42DAP/reference	0.7238	0.011
43DAP/reference	1.10101	0.575
47DAP/reference	0.89994	0.178
52DAP/reference	1.09616	0.168
57DAP/reference	1.42602	0.055

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.72035	0.017
17DAP/reference	1.1646	0.578
27DAP/reference	1.5792	0.028
39DAP/reference	1.4031	0.015
41DAP/reference	1.08379	0.734
42DAP/reference	1.0415	0.907
43DAP/reference	1.33504	0.186
47DAP/reference	0.92201	0.357
52DAP/reference	1.86093	0.228
57DAP/reference	0.78254	0.152

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00923	1
26DAP/20DAP	0.99881	1
34DAP/26DAP	1.00603	1
51DAP/34DAP	0.58172	0.061
52DAP/51DAP	1.1014	0.676
53DAP/52DAP	0.89485	0.772
55DAP/53DAP	1.05318	0.927
57DAP/55DAP	0.95821	0.817
62DAP/57DAP	1.0735	0.8
68DAP/62DAP	0.85301	0.668
68DAP/14DAP	0.66057	0.121

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92703	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.3799
Mature Eggplant/Ripe Tomato	1.71808	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09616	0.877
1-1-2/M82	1.0528	1
12-2/M82	1.42133
12-4/M82	1.24395	1
1-3/M82	0.77757
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.1481	0.425
3-2/M82	N/A	N/A
4-1-1/M82	1.12078
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.89225
5-3/M82	0.94287	1
6-2/M82	1.06426	0.253
6-3/M82	0.74476
7-1/M82	N/A	N/A
7-2/M82	0.94617
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.77097	0.337
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05699	1
IL12-4/WTpooled	1.17761	0.891
IL1-4/WTpooled	1.03624
WT/WTpooled	1.09899	0.957

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.85264	0.975

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.32645	0.921
DC3000/delta hrp 6h	0.63461	0.942
DC3000/delta hrp 12h	1.11782	1
DC3000/delta hrp 24h	1.32309	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.27402	0.183
DC3000 delta B/DC3000 delta AB	1.36628	0.129

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95712	1
Exp 36h	1.27551	0.693
Exp 60h	1.21205	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.09562
Var 0h	0.98759	1
Var 12h I row2-row1	1.1871	0.506
Var 12h NI row2-row1	1.15417	0.281
Var 36h I row2-row1	1.10507	1
Var 36h NI row2-row1	0.85459	0.61
Var 60h I row2-row1	0.75123	0.374
Var 60h NI row2-row1	1.09311	0.691
Time course 0hI-0hNI	1.04996	0.867
Time course 12hI-12hNI	1.05099	0.703
Time course 36hI-36hNI	1.09442	0.28
Time course 60hI-60hNI	1.1413	0.426

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.03727	0.408
transgenic ySAMdc/azygous control (breaker)	1.23169	1
transgenic ySAMdc/azygous control (red)	1.09279	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01099	0.395

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85202	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89488	1
Manapal/WT (break)	1.06947	1
Manapal/WT (red)	0.90934	0.274